Title: Designing Antimicrobial Peptide: Current Status

Author: Fahad Almsned

 DOI:  https://dx.doi.org/10.18535/jmscr/v5i3.153

Abstract

1. Introduction

Antimicrobial peptides (AMPs) are critical part of the human natural immunity, innate specifically, which is found among all modules of life. These peptides, which are produced by leukocytes, are working as broad-spectrum antibiotics that exhibit potential as novel therapeutic agents. AMPs have been confirmed to eliminate G-ve and G+ve bacteria, enveloped viruses, fungi, and even cancerous cells1. AMPs eliminate these invading objects by direct antimicrobial effect as well as other effects like suppressing bacterial protective biofilm formation and enhancing the bacterial elimination by phagocytosis2. AMPs, comparing to conventional antibiotics, may also have the ability to enhance immunity by functioning as immuno modulator through a variety of actions, like apoptotic control on immune cells, chemokine release by epithelial cells, enhancing wound healing, and many other actions that help promoting adaptive immunity3-4.

References

1.      Reddy KV, Yedery RD, Aranha C (2004). "Antimicrobial peptides: premises and promises". International Journal of Antimicrobial Agents24 (6): 536–547.

2.      van der Does, A. M. et al. Antimicrobial peptide hLF1–11 directs granulocyte-macrophage colony- stimulating factor-driven monocyte differentiation toward macrophages with enhanced recognition and clearance of pathogens. Antimicrob. Agents Chemother. 54, 811–816 (2010).

3.      Hancock R. E. W. &Sahl H. G. Antimicrobial and host- defense peptides as new anti-infective therapeutic strategies. Nature Biotech. 24, 1551–1557 (2006).

4.      Lehrer, R. I. Primate defensins. Nature Rev. Microbiol. 2, 727–738 (2004).

5.      Cooper MA, Shlaes D. Fix the antibiotics pipeline. Nature. 2011; 472:32.

6.      Steckbeck JD, Deslouches B, Montelaro RC.(2016) “Antimicrobial peptides: new drugs for bad bugs?”

7.      Smith, P. A. &Romesberg, F. E. Combating bacteria and drug resistance by inhibiting mechanisms of persistence and adaptation. Nature Chem. Biol. 3, 549–556 (2007).

8.      Friedrich, C. L., Rozek, A., Patrzykat, A. &Hancock, R. E. W. Structure and mechanism of action of an indolicidin peptide derivative with improved activity against Gram-positive bacteria. J. Biol. Chem. 276, 24015–24022 (2001).

9.      Fleitas O, Agbale CM, Franco OL, (2016) .”Bacterial resistance to antimicrobial peptides: an evolving phenomenon”

10.  Nguyen LT, Haney EF, Vogel HJ. The expanding scope of antimicrobial peptide structures and their modes of action. Trends Biotechnol. 2011; 29:464–72. [PubMed: 21680034]

11.  Zasloff M. Antimicrobial peptides of multicellular organisms. Nature. 2002; 415:389–95. [PubMed: 11807545]

12.  Hale JDF, Hancock REW. Alternative mechanisms of action of cationic antimicrobial peptides on bacteria. Expert Rev Anti Infect Ther. 2007; 5:951–9.

13.  Juneyoung Lee, Dong Gun Lee “Antimicrobial Peptides (AMPs) with Dual Mechanisms: Membrane Disruption and Apoptosis”. J. Microbiol. Biotechnol.2015 ; 25(6): 759~764.

14.  Matsuzaki K, Sugishita K, Harada M, Fujii N, Miyajima K. 1997. Interactions of an antimicrobial peptide, magainin 2, with outer and inner membranes of gram-negative bacteria. Biochim. Biophy. Acta 1327: 119-130.

15.  Lee W, Lee DG. 2014. Magainin 2 induces bacterial cell death showing apoptotic properties. Curr. Microbiol. 69: 794-801.

16.  Wimley, W. C. &Hristova, K. Antimicrobial peptides: successes, challenges and unanswered questions.

17.  Fjell CD, Hiss JA, Hancock REW, Schneider G. Designing antimicrobial peptides: form followsfunction. Nat Rev Drug Discov. 2012; 11:37–51. A comprehensive review of the current state of using computational tools to guide the AMP design process. [PubMed: 22173434]

18.  Zhang, L. et al. Interaction of polyphemusin I and structural analogs with bacterial membranes, lipopolysaccharide, and lipid monolayers. Biochemistry 39, 14504–14514 (2000).

19.  Miyata, T. et al. Antimicrobial peptides, isolated from horseshoe crab hemocytes, tachyplesin II, and polyphemusins I and II: chemical structures and biological activity. J. Biochem. 106, 663–668 (1989).

20.  Wang, G. S., Li, X., Zasloff, M “A database view of naturally occurring antimicrobial peptides: nomenclature, classification and amino acid sequence analysis.” 10.1079/9781845936570.0001

21.  Fjell, C. D., Hancock, R. E. W. & Cherk-asov, A. AMPer: a database and an auto-mated discovery tool for antimicrobial peptides. Bioinformatics 23, 1148–1155 (2007).

22.  Waghu FH, Barai RS, Gurung P, Idicula-Thomas S. CAMPR3: a database on sequences, structures and signatures of antimicrobial peptides. Nucleic Acids Res. 2015 : gkv1051v1-gkv1051. Epub 2015 Oct 13

23.  Wang, G., Li, X. and Wang, Z. (2016) APD3: the antimicrobial peptide database as a tool for research and education. Nucleic Acids Research 44, D1087-D1093.

24.  Juretić, D., Vukicević, D., Ilić, N., Antcheva, N. &Tossi, A. Computational design of highly selective antimicrobial peptides. J. Chem. Inf. Model. 49, 2873–2882 (2009).

25.  Ng X. Y., Rosdi B. A. &Shahrudin S. Prediction of Antimicrobial Peptides Based on Sequence Alignment and Sup-port Vector Machine-Pairwise Algorithm Utilizing LZ-Complexity. Biomed Res Int 2015, 212715 (2015).

26.  Bahar A. A. &Ren D. Antimicrobial peptides. Pharmaceuticals. 6, 1543–1575 (2013).

27.  Jenssen, H.; Hamill, P.; Hancock, R.E.W. Peptide antimicrobial agents. Clin. Microbiol. Rev. 2006, 19, 491–511.

28.  Westerhoff, H.V.; Juretic, D.; Hendler, R.W.; Zasloff, M. Magainins and the disruption of membrane-linked free-energy transduction. Proc. Natl. Acad. Sci. USA 1989, 86, 6597–6601.

29.  Park, Y.; Park, S.C.; Park, H.K.; Shin, S.Y.; Kim, Y.; Hahm, K.S. Structure-activity relationship of hp (2–20) analog peptide: Enhanced antimicrobial activity by n-terminal random coil regiondeletion. Biopolymers 2007, 88, 199–207.

30.  Jiang, Z.; Vasil, A.I.; Hale, J.D.; Hancock, R.E.; Vasil, M.L.; Hodges, R.S. Effects of net charge and the number of positively charged residues on the biological activity of amphipathic alpha-helical cationic antimicrobial peptides. Biopolymers 2008, 90, 369–383.

31.  Huang, Y.B.; Huang, J.F.; Chen, Y.X. Alpha-helical cationic antimicrobial peptides: Relationships of structure and function. Protein Cell 2010, 1, 143–152

32.  Oren, Z.; Shai, Y. A class of highly potent antibacterial peptides derived from pardaxin, apore-forming peptide isolated from moses sole fish Pardachirusmarm-oratus. Eur. J. Biochem 1996, 237, 303–310.

33.  Tossi, A.; Sandri, L.; Giangaspero, A. Amphipathic, alpha-helical antimicrobial peptides.Biopolymers 2000, 55, 4–30.

34.  Lee, D.G.; Kim, H.N.; Park, Y.K.; Kim, H.K.; Choi, B.H.; Choi, C.H.; Hahm, K.S. Design of novel analogue peptides with potent antibiotic activity based on the antimicrobial peptide,hp (2–20), derived from n-terminus of Helicobacter pylori ribosomal protein L1. Biochim.Biophys. Acta 2002, 1598, 185–194

35.  Dathe, M.; Wieprecht, T.; Nikolenko, H.; Handel, L.; Maloy, W.L.; MacDonald, D.L.;Beyermann, M.; Bienert, M. Hydrophobicity, hydrophobic moment and angle subtended by charged residues modulate antibacterial and haemolytic activity of amphipathic helical peptides.FEBS Lett. 1997, 403, 208–212.

36.  Fernandez-Vidal, M.; Jayasinghe, S.; Ladokhin, A.S.; White, S.H. Folding amphipathic helices into membranes: Amphiphilicity trumps hydrophobicity. J. Mol. Biol. 2007, 370, 459–470.

37.  G. Maccari, M. Di Luca, R. Nifosì ”In silico design of antimicrobial peptides” Methods Mol. Biol., 1268 (2015), pp. 195–219.

38.  Rathinakumar R, Wimley WC (2008) Biomolecular engineering by combina-torial design and high-throughput screening: small, soluble peptides that permeabilize membranes. J Am ChemSoc 130: 9849– 9858.

39.  Marks JR, Placone J, Hristova K, Wimley WC (2011) Spontaneous membrane-translocating peptides by orthogonal high-throughput screening. J Am ChemSoc 133: 8995– 9004.

40.  Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25– 29..

41.  Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide seque-nces. Bioinformatics 22: 1658– 1659.

42.  Thomas S, Karnik S, Barai RS, Jayaraman VK, Idicula-Thomas S (2010) CAMP: a useful resource for research on antimicrobial peptides. Nucleic Acids Res 38: D774– 80.

43.  Ebalunode, J. O., Zheng, W. &Tropsha, A. Application of QSAR and shape pharmacophore modeling approaches for targeted chemical library design. Methods Mol. Biol. 685, 111–133 (2011).

44.  Wold S, Jonsson J, Sjörström M, Sandberg M, Rännar S (1993) DNA and peptide sequences and chemical processes multivariately modelled by principal component analysis and partial least-squares projections to latent structures. Anal ChimActa 277: 239– 253.

45.  Jaiswal K, Naik PK (2008) Distinguishing compounds with anticancer activity by ANN using inductive QSAR descriptors. Bioinformation 2: 441– 451.

46.  Michaelson JJ, Sebat J (2012) forestSV: structural variant discovery through statistical learning. Nat Methods 9:819– 821.

47.  Peng H, Long F, Ding C (2005) Feature selection based on mutual information: criteria of max-dependency max-relev-ance, and min-redundancy. IEEE Trans Pattern Anal Mach Intell 27: 1226– 1238.

48.  Hansen L, Lee EA, Hestir K, Williams LT, Farrelly D (2009) Controlling feature selection in random forests ofdecision trees using a genetic algorithm: classification of class I MHC peptides. Comb Chem High Throughput Screen 12: 514– 519.

49.  Fjell CD, Jenssen H, Cheung WA, Hancock REW, Cherkasov A (2011) Optimization of antibacterial peptide by genetic algorithms and cheminformatics. Chem Biol Drug Des 77: 48– 56.

50.  Deb K, Pratap A, Agarwal S, Meyarivan T (2002) A fast and elitist multiobjective genetic algorithm: NSGA-II. IEEE Trans EvolComput 6: 182– 197.

51.  Alder, B. J.; Wainwright, T. E. (1959). "Studies in Molecular Dynamics. I. Gen-eral Method". J. Chem. Phys.31 (2): 459.

52.  Bocchinfuso G, Bobone S, Mazzuca C, Palleschi A, Stella L (2011) Fluorescence spectroscopy and molecular dynamics simulations in studies on the mechanism of membrane destabilization by antimicrobial peptides. Cell Mol Life Sci 68: 2281– 2301.

53.  Ponder JW, Case DA (2003) Force Fields for Protein Simulations. In: Daggett V, editor. Protein Simulations. Academic Press, Vol. 66. pp. 27– 85.

54.  Lindorff-Larsen K, Maragakis P, Piana S, Eastwood MP, Dror RO, et al. (2012) Systematic validation of protein force fields against experimental data. PLoS One 7: e32131.

55.  Monticelli L, Kandasamy SK, Periole X, Larson RG, Tieleman DP, et al. (2008) The MARTINI Coarse-Grained Force Field: Extension to Proteins. J Chem Theory Comput 4: 819– 834. doi:10.1021/ct700324x.

56.  Bennett WFD, Tieleman DP (2011) Water Defect and Pore Formation in Atomistic and Coarse-Grained Lipid Membranes : Pushing the Limits of Coarse Graining.

57.  Ayton GS, Noid WG, Voth G a (2007) Multiscale modeling of biomolecular systems: in serial and in parallel. Curr Opin Struct Biol 17: 192– 198. doi:10.1016/j.sbi.2007.03.004.

58.  Torrie GM, Valleau JP (1977) Nonp-hysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling. J Comput Phys 23: 187– 199. doi:10.1016/0021-9991(77)90121-8.

59.  Laio A, Parrinello M (2002) Escaping free-energy minima. Proc Natl AcadSci U S A 99: 12562– 12566. doi:10.1073/pnas.202427399.

60.  Yesylevskyy S, Marrink S-J, Mark AE (2009) Alternative mechanisms for the interaction of the cell-penetrating peptides penetratin and the TAT peptide with lipid bilayers. Biophys J 97: 40– 49.

61.  Sugita Y, Yuko Y (1999) Replica-exchange molecular dynamics method for protein folding.

62.  Maccari G, Di Luca M, Nifosí R, Cardarelli F, Signore G, et al. (2013) Antimicrobial peptides design by evolutionary multiobjective optimization. PLoS Comput Biol 9: e1003212.

63.  Langham A, Kaznessis YN (2010) Molecular simulations of antimicrobial peptides. Methods MolBiol 618:267– 285. doi:10.1007/978-1-60761-594-1_17.

64.  Venturoli M, Smit B (1999) Simulating the self-assembly of model membranes. Phys Chem Comm 2: 45 doi:10.1039/a906472i.

65.  Thøgersen L, Schiøtt B, Vosegaard T, Nielsen NC, Tajkhorshid E (2008) Peptide aggregation and poreformation in a lipid bilayer: a combined coarse-grained and all atom molecular dynamics study. Biophys J 95:4337– 4347.

66.  Peter Tieleman D, Hess B, Sansom MSP (2002) Analysis and Evaluation of Channel Models: Simulations of Alamethicin. Biophys J 83: 2393– 2407.

67.  Robinson, J. A. Protein epitope mimetics as anti-infectives. Curr. Opin. Chem. Biol. 15, 379–386 (2011).

68.  Wrede, P. & Schneider, G. (eds) Concepts in Protein Engineering and Design 281–317 (Walter-de‑Gruyter, Berlin, New York, 1994).

69.  Yasin, B.; Pang, M.; Turner, J.S.; Cho, Y.; Dinh, N.N.; Waring, A.J.; Lehrer, R.I.; Wagar, E.A.Evaluation of the inactivation of infectious herpes simplex virus by host-defense peptides. Eur. J.Clin. Microbiol. Infect. Dis. 2000, 19, 187–194.

70.  Uteng, M.; Hauge, H.H.; Markwick, P.R.; Fimland, G.; Mantzilas, D.; Nissen-Meyer, J.;Muhle-Goll, C. Three-dimensional structure in lipid micelles of the pediocin-like antimicrobialpeptidesakacin p and a sakacin p variant that is structurally stabilized by an inserted c-terminal disulfide bridge. Biochemistry 2003, 42, 11417–11426.

71.  Osapay, K.; Tran, D.; Ladokhin, A.S.; White, S.H.; Henschen, A.H.; Selsted, M.E. Formation and characterization of a single trp-trp cross-link in indolicidin that confers protease stability without altering antimicrobial activity. J. Biol. Chem. 2000, 275, 12017–12022.

72.  Zhang, L.; Benz, R.; Hancock, R.E. Influence of proline residues on the antibacterial and synergistic activities of alpha-helical peptides. Biochemistry 1999, 38, 8102–8111.

73.  Goblyos, A.; Schimmel, K.J.; Valentijn, A.R.; Fathers, L.M.; Cordfunke, R.A.; Chan, H.L.; Oostendorp, J.; Nibbering, P.H.; Drijfhout, J.W.; Hiemstra, P.S.; et al. Development of a nose cream containing the synthetic antimicrobial peptide p60.4ac for eradication of methicillin-resistant Staphylococcus aureus carriage. J. Pharm. Sci. 2013, 102, 3539–3544.

74.  Kim, J.Y.; Park, S.C.; Yoon, M.Y.; Hahm, K.S.; Park, Y. C-terminal amidation of pmap-23: Translocation to the inner membrane of gram-negative bacteria. Amino Acids 2011, 40, 183–195.

75.  180. Berthold, N.; Czihal, P.; Fritsche, S.; Sauer, U.; Schiffer, G.; Knappe, D.; Alber, G.; Hoffmann, R. Novel apidaecin 1b analogs with superior serum stabilities for treatment of infections by gram-negative pathogens. Antimicrob. Agents Chemother. 2013, 57, 402–409.

Corresponding Author

Fahad Almsned

School of Systems Biology, George Mason University, Fairfax, VA 22030

Email: This email address is being protected from spambots. You need JavaScript enabled to view it.